Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California

Erik R Hawley; Hailan Piao; Nicole M Scott; Stephanie Malfatti; Ioanna Pagani; Marcel Huntemann; Amy Chen; Tijana Glavina Del Rio; Brian Foster; Alex Copeland; Janet Jansson; Amrita Pati; Susannah Tringe; Jack A Gilbert; Thomas D Lorenson; Matthias Hess

doi:10.4056/sigs.5029016

Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California

Stand Genomic Sci. 2014 Jan 2;9(3):1259-74. doi: 10.4056/sigs.5029016. eCollection 2014 Jun 15.

Authors

Affiliations

¹ Washington State University Tri-Cities, Richland, WA, USA.
² Argonne National Laboratory, Lemont, IL, USA.
³ Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, CA, USA.
⁴ DOE Joint Genome Institute, Walnut Creek, CA, USA.
⁵ DOE Joint Genome Institute, Walnut Creek, CA, USA ; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁶ Argonne National Laboratory, Lemont, IL, USA ; University of Chicago, Chicago, IL, USA.
⁷ USGS, Menlo Park, CA, USA.
⁸ Washington State University Tri-Cities, Richland, WA, USA ; DOE Joint Genome Institute, Walnut Creek, CA, USA ; Washington State University, Pullman, WA, USA ; Pacific Northwest National Laboratory, Chemical & Biological Process Development Group, Richland, WA, USA ; Environmental Molecular Sciences Laboratory, Richland, WA, USA.

Abstract

Crude oils can be major contaminants of the marine ecosystem and microorganisms play a significant role in the degradation of its main constituents. To increase our understanding of the microbial hydrocarbon degradation process in the marine ecosystem, we collected crude oil from an active seep area located in the Santa Barbara Channel (SBC) and generated a total of about 52 Gb of raw metagenomic sequence data. The assembled data comprised ~500 Mb, representing ~1.1 million genes derived primarily from chemolithoautotrophic bacteria. Members of Oceanospirillales, a bacterial order belonging to the Deltaproteobacteria, recruited less than 2% of the assembled genes within the SBC metagenome. In contrast, the microbial community associated with the oil plume that developed in the aftermath of the Deepwater Horizon (DWH) blowout in 2010, was dominated by Oceanospirillales, which comprised more than 60% of the metagenomic data generated from the DWH oil plume. This suggests that Oceanospirillales might play a less significant role in the microbially mediated hydrocarbon conversion within the SBC seep oil compared to the DWH plume oil. We hypothesize that this difference results from the SBC oil seep being mostly anaerobic, while the DWH oil plume is aerobic. Within the Archaea, the phylum Euryarchaeota, recruited more than 95% of the assembled archaeal sequences from the SBC oil seep metagenome, with more than 50% of the sequences assigned to members of the orders Methanomicrobiales and Methanosarcinales. These orders contain organisms capable of anaerobic methanogenesis and methane oxidation (AOM) and we hypothesize that these orders - and their metabolic capabilities - may be fundamental to the ecology of the SBC oil seep.

Keywords: Bioremediation; anaerobic methane oxidation; archaea; bacteria; crude oil; hydrocarbon-degradation; marine ecosystem; metagenomics; natural oil seeps.